Job ID = 6453603 SRX = SRX1299929 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:26:26 prefetch.2.10.7: 1) Downloading 'SRR2546848'... 2020-06-21T08:26:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:26:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:26:57 prefetch.2.10.7: 'SRR2546848' is valid 2020-06-21T08:26:57 prefetch.2.10.7: 1) 'SRR2546848' was downloaded successfully 2020-06-21T08:26:57 prefetch.2.10.7: 'SRR2546848' has 0 unresolved dependencies Read 1639581 spots for SRR2546848/SRR2546848.sra Written 1639581 spots for SRR2546848/SRR2546848.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:19 1639581 reads; of these: 1639581 (100.00%) were unpaired; of these: 1024308 (62.47%) aligned 0 times 326687 (19.93%) aligned exactly 1 time 288586 (17.60%) aligned >1 times 37.53% overall alignment rate Time searching: 00:00:19 Overall time: 00:00:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 204110 / 615273 = 0.3317 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:28:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:28:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:28:05: #1 total tags in treatment: 411163 INFO @ Sun, 21 Jun 2020 17:28:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:28:05: #1 tags after filtering in treatment: 410701 INFO @ Sun, 21 Jun 2020 17:28:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:06: #2 number of paired peaks: 1532 INFO @ Sun, 21 Jun 2020 17:28:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:06: #2 predicted fragment length is 235 bps INFO @ Sun, 21 Jun 2020 17:28:06: #2 alternative fragment length(s) may be 68,80,160,235,277 bps INFO @ Sun, 21 Jun 2020 17:28:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.05_model.r INFO @ Sun, 21 Jun 2020 17:28:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.05_summits.bed INFO @ Sun, 21 Jun 2020 17:28:08: Done! pass1 - making usageList (385 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 12 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:28:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:28:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:28:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:28:35: #1 total tags in treatment: 411163 INFO @ Sun, 21 Jun 2020 17:28:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:28:35: #1 tags after filtering in treatment: 410701 INFO @ Sun, 21 Jun 2020 17:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:35: #2 number of paired peaks: 1532 INFO @ Sun, 21 Jun 2020 17:28:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:35: #2 predicted fragment length is 235 bps INFO @ Sun, 21 Jun 2020 17:28:35: #2 alternative fragment length(s) may be 68,80,160,235,277 bps INFO @ Sun, 21 Jun 2020 17:28:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.10_model.r INFO @ Sun, 21 Jun 2020 17:28:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.10_summits.bed INFO @ Sun, 21 Jun 2020 17:28:37: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:29:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:29:03: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:29:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:29:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:29:05: #1 total tags in treatment: 411163 INFO @ Sun, 21 Jun 2020 17:29:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:29:05: #1 tags after filtering in treatment: 410701 INFO @ Sun, 21 Jun 2020 17:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:06: #2 number of paired peaks: 1532 INFO @ Sun, 21 Jun 2020 17:29:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:06: #2 predicted fragment length is 235 bps INFO @ Sun, 21 Jun 2020 17:29:06: #2 alternative fragment length(s) may be 68,80,160,235,277 bps INFO @ Sun, 21 Jun 2020 17:29:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.20_model.r INFO @ Sun, 21 Jun 2020 17:29:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299929/SRX1299929.20_summits.bed INFO @ Sun, 21 Jun 2020 17:29:08: Done! pass1 - making usageList (48 chroms): 0 millis pass2 - checking and writing primary data (61 records, 4 fields): 4 millis CompletedMACS2peakCalling